I don't know about the oil pans off the top of my head, but I do know about the transmissions.
The S38/M88 use the standard M30 bellhousing bolt pattern, so any M30 transmission can be bolted up. As such, rather than trying to use the Getrag 280, most people use the Getrag 265. (either flavor, but the close ratio box is significantly weaker than the overdrive version and is more expensive)
Using the 265 lets you drive the speedo just like the original transmission, although units from an E30 M3 lack the mechanical speedo drive. Most people just use an older one, which does have the drive. It ends up making things much easier. However, since you are also doing some diff work, that may not be the best option, as the stock speedo mechanism has no provision for altering the differential ratio.
Speaking of the diff, the easiest setup is to transplant the entire rear subframe from an E28 535. It bolts up and lets you use the much cheaper (and arguably more robust) front-loader diffs used in BMWs from the E28 on. That should significantly decrease the amount of welding required for that work. Also, if you use the later diff, it will have the speed sensor in the housing.
If you want to convert the speedo to an electronic unit, so you can use the stock BMW diff speed sensor used in later diffs, a good instrumentation shop should be able to do it. I've seen good results on this board from Hollywood Speedometer. (
http://www.nhspeedometer.com/)
As far as the tachometer signal, the S38B36 and the M88 use a single coil/distributor system, just like the original M30. There should be no problems with that. However, if you switch to the S38B38, that uses a coil-on-plug system, which would require some additional work. I know of no one using this engine, so I can't say too much about it.
You shouldn't need to use a different driveshaft, but any driveshaft you do use will need to be altered to fit the setup you described. It may need to be shortened, lengthened, or have different flanges welded on. Either way, you are not going to be able to use a stock, unaltered driveshaft for this project. The stock driveshaft is plenty strong, if that is what you are concerned about.